Background and aims: alpha- Fetoprotein ( AFP), a tumour marker for hepatocellular carcinoma ( HCC), is associated with poor prognosis. Using cDNA microarray analysis, we previously found that ephrin- A1, an angiogenic factor, is the most differentially overexpressed gene in AFP producing hepatoma cell lines. In the present study, we investigated the significance of ephrin- A1 expression in HCC. Methods: We examined ephrin- A1 expression and its effect on cell proliferation and gene expression in five AFP producing hepatoma cell lines, three AFP negative hepatoma cell lines, and 20 human HCC specimens. Results: Ephrin- A1 expression levels were lowest in normal liver tissue, elevated in cirrhotic tissue, and further elevated in HCC specimens. Ephrin- A1 expression was strongly correlated with AFP expression ( r = 0.866). We showed that ephrin- A1 induced expression of AFP. This finding implicates ephrin- A1 in the mechanism of AFP induction in HCC. Ephrin- A1 promoted the proliferation of ephrin- A1 underexpressing HLE cells, and an ephrin- A1 antisense oligonucleotide inhibited the proliferation of ephrin- A1 overexpressing Huh7 cells. Thus ephrin- A1 affects hepatoma cell growth. cDNA microarray analysis showed that ephrin- A1 induced expression of genes related to the cell cycle ( p21), angiogenesis ( angiopoietin 1 and thrombospondin 1), and cell- cell interactions ( Rho, integrin, and matrix metalloproteinases) in cultured hepatoma cells. These ephrin- A1 induced genes are also activated in HCC tissues that overexpress AFP. Conclusion: These findings suggest that the poor prognosis of patients with AFP producing HCC is partially caused by ephrin- A1 expression, which induces expression of genes related to tumour cell growth, angiogenesis, invasion, and metastasis.